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Illumina v. Ariosa – The “Bucket” to be in

Today, a divided Fed. Cir. panel reversed the district court’s decision invalidating the claim of two Illumina patents, U.S. Pat. Nos. 9,580,751 and 9,738,931, as directed to a natural phenomenon (Illumina, Inc. v. Ariosa Diagnostics, Inc., Appeal No. 2019-1419 (Fed. Cir., March 17, 2020, Judges Lourie and Moore, with Lourie writing, Judge Reyna dissenting).

The inventors had discovered that cell-free, fetal DNA, although a tiny fraction of maternal DNA, could be separated from maternal DNA on the basis of its molecular weight. In other words, cffDNA is approximately 500 base pairs or less, while maternal DNA is of a greater size. Claim 1 of the ‘751 patent reads as follows:

“1. A method for preparing a [DNA] fragment from a pregnant human female useful for analyzing a genetic locus involved in a fetal chromosomal aberration, comprising

(a) extracting DNA from a substantially cell-free sample of blood plasma or blood serum from a pregnant human female to obtain extracellular circulatory fetal and maternal DNA fragments;

(b) producing a fraction of the DNA extracted in (a) by:

i. size discrimination of extracellular DNA fragments; and

ii. selectively removing the DNA fragments greater than approximately 500 base pairs,

wherein the DNA fraction after (b) comprises a plurality of genetic loci of the extracellular circulatory fetal and maternal DNA; and

(c) analyzing a genetic locus in the fraction of DNA produced in (b).”

The panel marched through the tattered history of s. 101 jurisprudence and arrived at the Mayo/Alice test in Part I of the opinion but got right down to work in Part II:

“This is not a diagnostic case [ed. note: ignoring step (c)  of the claim?] And it is not a method of treatment case. It is a method of preparation case….The focus of the dispute in this case is whether the claims of the [patents] are ‘directed to’ the natural phenomenon, i.e., whether they claim the discovered natural phenomenon {that cell-free fetal DNA tends to be shorter than cell-free maternal DNA in a mother’s bloodstream] versus eligible subject matter that exploits the discovery of the natural phenomenon….[The recited] process steps change the composition of the mixture, resulting in a DNA fraction that is different from the naturally-occurring fraction in the mother’s blood. Thus, the process achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon…[The inventors exploited] that discovery in a method for preparation of a mixture enriched in fetal DNA.”

Now, all that remains is to distinguish Ariosa and its ill-fated associates, Mayo, Athena and Cleveland Clinic and get into the bucket provided by CellzDirect:

“We found [the Ariosa] claims ineligible because, like the invalid diagnostic claims at issue in Mayo, Athena and Cleveland Clinic, they were directed to detecting a natural phenomenon. In essence, the inventors in Ariosa discovered that cell-free fetal DNA exists, and then obtained patent claims that covered only the knowledge the cell-free fetal DNA exists and a method to see that it exists.”

Myriad was distinguished since the claims there covered “a gene rather than a process for isolating it. CellzDirect has been like an beautiful atoll that is surrounded by shark-infested legal waters but, at last, a Fed. Cir. panel once again makes it ashore:

“We found that [CellzDirect’s] claimed invention was patent-eligible because it was ‘not simply an observation or detection of the ability of hepatocytes to survive multiple free-thaw cycles. Rather, the claims are directed to a new and useful method of preserving hepatocyte cells.” That is, by isolating the hardy ones that could survive freeze-thaw cycles. The panel continues: “And, like in CellzDirect, the inventors used their discovery to invent a method of preparing a fraction of DNA that includes physical process steps to selectively remove some maternal DNA in blood to product a mixture enriched in fetal DNA.”

The fact that the inventors used conventional techniques and equipment doesn’t matter if you can stay at the first step of the Mayo/Alice inquiry and that is just how the panel left it:

“Rather than focusing on what the inventors of the [patents] did not invent, we focus our Alice/Mayo  step one analysis on what the inventors did purport to invent and what they claimed in their patents. Those [fractionation] methods ‘are directed to’ more than merely the natural phenomenon that the inventors discovered. Accordingly, we conclude at step one of the Alice/Mayo test that the claims are not directed to a patent-ineligible concept, and we need not reach step two of the test….The inventors here patented methods of preparing a DNA fraction. The claimed methods utilize the natural phenomenon that the inventors discovered by employing physical process steps to selectively remove larger fragments of cell-free DA and thus enrich a mixture in cell-free fetal DNA.”

Judge Reyna’s dissenting opinion is as long as the majority’s opinion. This technology is not in his wheelhouse but he believes that the claims were directed to the natural phenomenon and thus must be evaluated under step two of the Alice/Mayo test – and you know how that would turn out. However, the logic gets a bit lost right out of the bucket. Reyna writes: “Other than the surprising discovery, nothing else in the specification indicates that there was anything new or useful about the claimed invention. However in the same paragraph he writes: “The results in Example 2 demonstrate that fetal alleles for ‘D21S11,” a genetic marker found in the human chromosome related to Down Syndrome, could be detected in cell-free DNA samples from which fragments greater than 500 base pairs or 300  base pairs had been removed.” This look a lot like “new and useful” to me. Reyna calls this a “potential application” but this application would not exist but for the claimed method to prepare necessary DNA fraction.

He also disputes the majority’s attempt to distinguish Ariosa. Because the Ariosa claims and the present claims “begin and end with a naturally occurring substance, and [in his opinion] the claimed method steps do not alter those substances” the claimed method “is therefore directed to a natural phenomenon.” He shows how broadly he would read step one: “Because the patent’s claimed advance is the discovery of the natural phenomenon, the claims are directed to a natural phenomenon under the step one inquiry.” That’s simply “too broad an interpretation of this exclusionary principle [that] could eviscerate patent law.” In fact, such interpretations of s. 101 have been eviscerating patent law since Bilski, a decade ago. This is a pleasant break from this legal desert.

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